SfePy

sfepy@python.org

2 participants
880 discussions

sfepy-view problems
by Claus Kiefer 06 Dec '22

06 Dec '22

Dear sfepy-Experts I'm working with python 3.10 on Ubuntu 18.04 and when I try *sfepy-view navier_stokes.vtk* I get the error message ValueError: Invalid style "". Must be one of the following: "surface" "wire frame" "points". *The modules were installed using:* conda create -n EM python=3.10 conda activate EM conda install -c anaconda scipy pip install meshio pip install pyvista in the sfepy root-dir.: pip install . --user What's wrong ? kind regards, Claus

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Build and use sfepy
by Zicheng Wang 29 Nov '22

29 Nov '22

Dear developers, My name is Zicheng Wang. I've got two issues regarding installation of sfepy and hope you can help me. 1. two libraries namely slepc4py and petsc4py are not successfully installed in Microsoft windows system in which I am currently use. Is there any misfunction would happen while using sfepy for solving PDEs? 2. An error occurred: import Error: cannot import name 'show_config' from 'numpy'(unknown location) Many thanks in advance. Zicheng Wang, Kind regards

2 1

Installation on Windows using Anaconda
by Mauro Sgroi 22 Nov '22

22 Nov '22

Dear developers, my name is Mauro Sgroi and I would like to use sfepy to teach FEM. I installed the package using conda. Should I also compile the C modules separately or are they precompiled? Thanks a lot and best regards, Mauro Sgroi.

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Installation error - RuntimeError: tables is missing
by Joshua Meggitt 22 Nov '22

22 Nov '22

Hello sfepy! I am having trouble installing sfepy on my M1 mac using pip – I am getting an error which I am struggling to decode – it seems to be suggesting I don’t have pytables installed, but I do… joshuameggitt@joshuas-mbp-2 bin % pip3 install sfepy -v Using pip 22.3.1 from /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip (python 3.9) Collecting sfepy Using cached sfepy-2022.3.tar.gz (16.1 MB) Running command pip subprocess to install build dependencies Collecting setuptools<60.0 Using cached setuptools-59.8.0-py3-none-any.whl (952 kB) Collecting wheel Using cached wheel-0.38.4-py3-none-any.whl (36 kB) Collecting Cython<3.0,>=0.29.30 Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB) Collecting matplotlib Using cached matplotlib-3.6.2-cp39-cp39-macosx_11_0_arm64.whl (7.2 MB) Collecting meshio Using cached meshio-5.3.4-py3-none-any.whl (167 kB) Collecting oldest-supported-numpy Using cached oldest_supported_numpy-2022.11.19-py3-none-any.whl (4.9 kB) Collecting pyparsing Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB) Collecting scipy Using cached scipy-1.9.3-cp39-cp39-macosx_12_0_arm64.whl (28.6 MB) Collecting tables Using cached tables-3.7.0-cp39-cp39-macosx_10_9_universal2.whl Collecting contourpy>=1.0.1 Using cached contourpy-1.0.6-cp39-cp39-macosx_11_0_arm64.whl (226 kB) Collecting cycler>=0.10 Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting fonttools>=4.22.0 Using cached fonttools-4.38.0-py3-none-any.whl (965 kB) Collecting numpy>=1.19 Using cached numpy-1.23.5-cp39-cp39-macosx_11_0_arm64.whl (13.4 MB) Collecting python-dateutil>=2.7 Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting kiwisolver>=1.0.1 Using cached kiwisolver-1.4.4-cp39-cp39-macosx_11_0_arm64.whl (63 kB) Collecting pillow>=6.2.0 Using cached Pillow-9.3.0-cp39-cp39-macosx_11_0_arm64.whl (2.9 MB) Collecting packaging>=20.0 Using cached packaging-21.3-py3-none-any.whl (40 kB) Collecting rich Using cached rich-12.6.0-py3-none-any.whl (237 kB) Collecting numpy>=1.19 Using cached numpy-1.21.0-cp39-cp39-macosx_11_0_arm64.whl (12.1 MB) Collecting numexpr>=2.6.2 Using cached numexpr-2.8.4-cp39-cp39-macosx_11_0_arm64.whl (89 kB) Collecting six>=1.5 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting pygments<3.0.0,>=2.6.0 Using cached Pygments-2.13.0-py3-none-any.whl (1.1 MB) Collecting commonmark<0.10.0,>=0.9.0 Using cached commonmark-0.9.1-py2.py3-none-any.whl (51 kB) Installing collected packages: commonmark, wheel, six, setuptools, pyparsing, pygments, pillow, numpy, kiwisolver, fonttools, Cython, cycler, scipy, rich, python-dateutil, packaging, oldest-supported-numpy, numexpr, contourpy, tables, meshio, matplotlib ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. nbconvert 7.1.0 requires jupyter-core>=4.7, which is not installed. Successfully installed Cython-0.29.32 commonmark-0.9.1 contourpy-1.0.6 cycler-0.11.0 fonttools-4.38.0 kiwisolver-1.4.4 matplotlib-3.6.2 meshio-5.3.4 numexpr-2.8.4 numpy-1.21.0 oldest-supported-numpy-2022.11.19 packaging-21.3 pillow-9.3.0 pygments-2.13.0 pyparsing-3.0.9 python-dateutil-2.8.2 rich-12.6.0 scipy-1.9.3 setuptools-59.8.0 six-1.16.0 tables-3.7.0 wheel-0.38.4 Installing build dependencies ... done Running command Getting requirements to build wheel Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 162, in get_requires_for_build_wheel return self._get_build_requires( File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 143, in _get_build_requires self.run_setup() File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 267, in run_setup super(_BuildMetaLegacyBackend, File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 158, in run_setup exec(compile(code, __file__, 'exec'), locals()) File "setup.py", line 214, in <module> check_versions() File "setup.py", line 106, in check_versions package_check('tables', INFO.PYTABLES_MIN_VERSION, File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-install-6wjrcx5t/sfepy_ed194f740f8244c08f12a5b98619886b/./tools/build_helpers.py", line 314, in package_check raise RuntimeError(msgs['missing'] % pkg_name) RuntimeError: tables is missing error: subprocess-exited-with-error × Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output. note: This error originates from a subprocess, and is likely not a problem with pip. full command: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3 /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/tmpbv5i16rb cwd: /private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-install-6wjrcx5t/sfepy_ed194f740f8244c08f12a5b98619886b Getting requirements to build wheel ... error error: subprocess-exited-with-error × Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output. note: This error originates from a subprocess, and is likely not a problem with pip. Any advice on what I could try to do to fix this issue would be greatly appreciated! BR Josh [University of Salford] Dr Joshua WR Meggitt Lecturer in Acoustical Engineering 1st Floor Newton Building, Room 105 University of Salford, Greater Manchester M5 4WT T: +44(0) 161 2955208 j.w.r.meggitt1(a)salford.ac.uk<mailto:j.w.r.meggitt1@salford.ac.uk> / www.salford.ac.uk<http://www.salford.ac.uk/> [cid66978*image002.jpg(a)01D7EB5C.B9BEB240] Click here to book a personal tutoring appointment!<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Foutlook.o…> Researchgate: https://www.researchgate.net/profile/Joshua_Meggitt<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.resea…> Google Scholar: https://scholar.google.co.uk/citations?user=0KmpklkAAAAJ&hl=en&oi=sra<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.g…> Orchid: https://orcid.org/0000-0002-6665-2939<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org…> Latest Journal Articles: Interval sensitivity analysis of joint dynamics in complex built-up structures – JVC 2022<https://journals.sagepub.com/doi/10.1177/10775463221113969> Interval-based identification of response-critical joints: A tool for model refinement – JSV 2022<https://www.sciencedirect.com/science/article/pii/S0022460X22000979?via%3Di…> Generalised round-trip identity - For the determination of structural dynamic properties at locations inaccessible or too distant for direct measurement – JSV 2021<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> Vibro-acoustic analysis of a domestic product based on experimental measurement and hybrid modelling – AA 2021<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2…> Component Replacement TPA: a transmissibility-based structural modification method for in-situ transfer path analysis – JSV 2021<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww-scien…>

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Problem with sfepy-view
by Chris Walker 11 Oct '22

11 Oct '22

Hello, I am using the latest version of sfepy on Windows 11. Python 3.9.13 I went through the tutorial example OK, but when I get to sfepy-view, I get: sfepy-view cylinder.vtk Fatal error in launcher: Unable to create process using '"D:\bld\sfepy_1664559573405\_h_env\python.exe" "C:\Users\ChrisWalker\anaconda3\Scripts\sfepy-view.exe" cylinder.vtk': The system cannot find the file specified. It looks as if sfpey-view is trying to run python from the D: drive, but I have no D: drive. Thanks in advance Chris

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ANN: SfePy 2022.3
by Robert Cimrman 29 Sep '22

29 Sep '22

I am pleased to announce the release of SfePy 2022.3. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by finite element methods. It is distributed under the new BSD license. Home page: https://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - reorganized scripts - PyPI support - speed-up of linear elastodynamics problems - improved homogenization-based recovery of micro-scale solutions For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Yves Delley Vladimir Lukes

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Exerting two or more loading conditions
by kshargh.ali＠gmail.com 19 Sep '22

19 Sep '22

Hi all, To mimic a uniaxial tensile loading, I used "displacement = EssentialBC('displacement', gamma2, {'u.0' : disp_fun})" command before while the other end is fixed. Now, let's say I want to simultaneously stretch it along the y direction (i.e. assume I define another region gamma3 on the top edge). I was wondering how I should modify this code. I tried something like " displacement = EssentialBC('displacement', gamma2, {'u.0' : disp_fun}, gamma3, {'u.1' : disp1_fun})" and different variation but I didn't have any success. Thus, I was wondering if you could please help me out with this. Best, Ali

2 1

PyPI support and reorganized scripts
by Robert Cimrman 12 Sep '22

12 Sep '22

Hi all, the next release (2022.3, due to the end of September) will contain several important user-oriented changes. Originally, the sfepy package was meant to be used mostly in-place in the source tree - the main scripts were directly there. In order to facilitate the installed use as well as to allow using pip, the scripts now reside in sfepy/scripts/ directory and new entry points are installed to the executable path. Short summary (<path> is the path to the sfepy directory relative to the users directory): python3 <path>/simple.py example.py -> sfepy-run example.py python3 <path>/resview.py example.py -> sfepy-view example.py python3 <path>/script/convert_mesh.py -d 3 mesh1.mesh mesh1.vtk -> sfepy-convert -d 3 mesh1.mesh mesh1.vtk python3 <path>/script/blockgen.py -> sfepy-mesh block python3 <path>/script/show_mesh_info.py cylinder.vtk -> sfepy-mesh info cylinder.vtk A pre-release version with the above changes is available on PyPI, you can try it with pip install sfepy (or "python3 -m pip install sfepy") It should install sfepy and all its required dependencies. Some optional solvers are not installed automatically (e.g. petsc4py or scikit-umfpack). The installation can be tested using python3 -c "import sfepy; sfepy.test()" Feedback welcome. Best regards, r.

1 0

sfepy-convert problem
by Christopher Walker 10 Sep '22

10 Sep '22

Hello, I am newbie to sfepy. I am using Windows 10 and python 3.9.1 (I also tried some earlier python versions to see if that helped). I was following the instructions for "Preprocessing: FreeCAD/OpenSCAD + Gmsh" that can be found here: https://sfepy.org/doc-devel/preprocessing.html I got as far as this command: sfepy-convert -d 3 screwdriver_handle.msh screwdriver_handle.vtk but the command was not recognised. However, the command sfepy-run is recognised I was wondering whether this was because I needed to compile the C extension modules (which I had not done). I tried executing the command python setup.py build_ext --inplace from the top level sfepy directory, which, on my system, I believe to be here (at least that is where I found the setp.py file): C:\Users\ChrisWalker\anaconda3\pkgs\sfepy-2022.2-py39h5d4886f_0\Lib\site-packages\sfepy but I get a load of error messages starting with: Appending sfepy.applications configuration to sfepy Ignoring attempt to set 'name' (from 'sfepy' to 'sfepy.applications') Appending sfepy.base configuration to sfepy Ignoring attempt to set 'name' (from 'sfepy' to 'sfepy.base') non-existing path in 'discrete\\common\\extmods': 'fmfield.c' non-existing path in 'discrete\\common\\extmods': 'refmaps.c' etc etc I expect I am making some schoolboy errors here, but I cannot spot it. Is anyone able to help ? Thanks Chris

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Re: About the stiffness matrix
by jhchen 06 Sep '22

06 Sep '22

Hi Robert: I’ve been able to get the stiffness matrix under your help, but I still get several puzzles about the linear system components [1] (8): Is the linear system in the matrix formula: Kx=r ? I exported both K and r to matlab to used the right division to get x: x = r \ K. But this gave me a different result from variables = pb.solve() and x = variables.vec. Analysis showed that pb.solve() gave the appropriate result, what’s the difference between the two approaches? In my project, the measurements (knowns) are Φ on surface (∂Ω) and the unknown is the source distribution Q in attached ProblemDescription.docx. So I need to separate the vectors Φ and Q (nodal values of Φ(x) and Q(x)) explicitly in the matrix form, which means I need to get the matrix F: (FQ is the discretized form of ∫_Ω▒Q(x)s(x)dx in (2), where Q(x) is the source distribution, s(x) is the test function). How can I get this matrix? I found that the solver in SfePy was much faster than the right division in matlab, so I’m curious that which function does SfePy adopts to solve the linear system. Besides, my project requires the inversion of a sub-matrix of the stiffness matrix K, does SfePy offer such methods or which function do you recommend to invert such a banded sparse matrix?

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